Abstract 2073: Genomics to Notebook (g2nb): Extending the electronic notebook to address the needs of cancer bioinformatics
Authors: Michael M. Reich, Thorin Tabor, John Liefeld, Jayadev Joshi, Forrest Kim, Helga Thorvaldsdottir, Daniel Blankenberg, Jill P. Mesirov
Journal: Cancer Research (2023)

Abstract As the availability of genomic data and analysis tools from large-scale cancer initiatives continues to increase, with single-cell studies adding new dimensions to the potential scientific insights, the need has become more urgent for a software environment that supports the rapid pace of cancer data science. The The Jupyter Notebook environment has become the de facto medium for this purpose due to its ease in combining scientific exposition with executable code to form a single reproducible “research narrative” document. However, analyses are often compute-intensive, requiring more resources than are frequently available within a notebook environment running on a desktop or laptop computer. Additionally, thousands of tools, modules, and plugins are readily available on integrative software platforms such as Galaxy, GenePattern, and Cytoscape, outside the notebook paradigm. Finally, many biomedical investigators lack the programming expertise required to fully realize the benefits and utility of the notebook metaphor. To address these issues, we have released Genomics to Notebook (g2nb), which builds on JupyterLab to add access to bioinformatics platforms and other functionality for the non-programmer through the components described below, while retaining all programmatic features of JupyterLab.The g2nb environment incorporates bioinformatics software platforms within the notebook interface, allowing a single notebook to contain a workflow spanning multiple tools and servers. When run, the entire analysis appears to execute seamlessly within the notebook. To achieve this, we developed a new analysis cell type that provides an interface within the notebook to tools that are hosted on a remote Galaxy or GenePattern server. Analysis cells present a web form-like interface, similar to that of the original platforms, requiring an investigator to provide only the input parameters and data. The popular visualization tools Cytoscape and Integrative Genomics Viewer (IGV) are also supported in their web-based formats as notebook cells, with additional platforms and visualizers added regularly. The g2nb environment is freely available at the g2nb workspace, http://g2nb.org, where scientists can use all of the g2nb functionality with only a web browser. Those who wish to use g2nb locally can use the provided Docker container or install the packages via the conda or pip package managers. The online workspace also includes a library of featured genomic analysis notebooks, including templates for common analysis tasks as well as cancer-specific research scenarios and compute-intensive methods. Scientists can easily copy these notebooks, use them as is, or adapt them for their research purposes. Citation Format: Michael M. Reich, Thorin Tabor, John Liefeld, Jayadev Joshi, Forrest Kim, Helga Thorvaldsdottir, Daniel Blankenberg, Jill P. Mesirov. Genomics to Notebook (g2nb): Extending the electronic notebook to address the needs of cancer bioinformatics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2073.